Notes

Notes

• Schedule updated: tomorrow Exp.2 pre-lab

• Lab report– Citations:

• Think about intellectual contribution• Lab notebook definitely needs cited

• Henderson-Hasselbalch– I owe you some additional practice problems

• To be added to website soon

Chapter 3

• Reading– Won’t cover details of Edman degradation-

mediated protein sequencing (part of 3.4)– Won’t cover Chapter 3.5 (yet)

• Suggested HW– 2, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 18

Condensation of two amino acids to form a peptide bond

-COOH + NH2- → C║O

N

HH2O+

“Peptide” bond: amideLarge positive G: amino acids need to be “activated”

Amino terminusN-terminus

Carboxyl terminusC-terminus

Peptide bond

Proteins/polypeptides are polymers of amino acids

N-terminus

C-terminus

-carbonamino group (basic) carboxylic group (acidic)R group (gives the amino acid its identity)

Generic -amino acid

(Most) amino acids have a stereocenter“L” isomer: L for life

20 ‘common’ amino acids

• Make up vast majority of amino acids in natural proteins

• Coded for in the genetic code

• Other amino acids:– Posttranslational modifications– Intermediates in metabolic pathways

Two main groups of side chains (plus subgroups)

• Nonpolar (hydrophobic)– Aliphatic (non-aromatic, mostly straight chains)– Aromatic (conjugated ring structures)

• Polar (hydrophilic)– Uncharged

• Hydrogen bonds

– Positively charged• “basic”

– Negatively charged• “acidic”

At physiologic pH (~7)

Things to know about amino acids

1. Name

2. R-group structure

3. R-group classification

4. Three-letter abbreviations

5. One-letter abbreviations

Two cysteine residues oxidize to form a disulfide bond

-Covalent bond: stronger than a hydrogen bond-Reversible: readily reduced back to free sulfhydryls

Free amino acid: “acid” & “base”

pI: “isoelectric point”

pH at which the species has no net charge

No net mvmt within electric gradient

+1 +1

-1-1

Uncharged side chain:

pI = ½ (pK(NH3+) + pK(COOH))

10.5

0-0.5

-1

+

+

+

+

+---

0

0

0

0+2 +1 0 -1

+1.5 +0.5 -0.5

pI between pKR and pK2

Free amino acid vs. polymers

• Terminology– Dipeptide (two amino acids)

• Tri-, tetra-, penta-peptide (etc)

– Oligopeptide (several a.a. ~3-30?)– Polypeptide (multiple a.a.)– Protein (multiple a.a.)

Free amino acid vs. polymers

Pentapeptide (five carbons!)What’s the charge at pH=7?